GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgK in Pseudomonas fluorescens GW456-L13

Align 2-dehydro-3-deoxygluconokinase; 2-keto-3-deoxygluconokinase; 3-deoxy-2-oxo-D-gluconate kinase; KDG kinase; EC 2.7.1.45 (characterized)
to candidate PfGW456L13_2950 2-ketogluconate kinase (EC 2.7.1.13)

Query= SwissProt::P50845
         (324 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2950
          Length = 328

 Score =  307 bits (786), Expect = 3e-88
 Identities = 159/313 (50%), Positives = 215/313 (68%), Gaps = 3/313 (0%)

Query: 2   KLDAVTFGESMAMFYANEYGGLHEVSTFSKGLAGAESNVACGLARLGFRMGWMSKVGNDQ 61
           ++D ++FGE+MAMF A + G L  V+ F K +AGA+SNVA GL+RLGF + W+S+VG D 
Sbjct: 3   EIDILSFGETMAMFVAEQTGDLASVNEFHKRIAGADSNVAIGLSRLGFNVAWLSRVGADS 62

Query: 62  LGTFILQELKKEGVDVSRVIRSQDENPTGLLLKSKVKEG-DPQVTYYRKNSAASTLTTAE 120
           LG F++  L+KEG+D  R +     +PTG  LKS+  +G DP V Y+R+ SAAS L++  
Sbjct: 63  LGRFVIDTLEKEGLDC-RHVDIDPAHPTGFQLKSRTDDGSDPVVEYFRRGSAASHLSSHS 121

Query: 121 YPRDYFQCAGHLHVTGIPPALSAEMKDFTYHVMNDMRNAGKTISFDPNVRPSLWPDQATM 180
              D  + A HLH TGIP ALS   +  ++ +M  MR+AG+++SFDPN+RPSLW  +  M
Sbjct: 122 IVPDLLK-ARHLHATGIPAALSETARQMSFELMTRMRDAGRSVSFDPNLRPSLWASERLM 180

Query: 181 VHTINDLAGLADWFFPGIAEGELLTGEKTPEGIADYYLKKGASFVAIKLGKEGAYFKTGT 240
           +  IN LA LA W  PG++EG LLTG + P  IA +YL +GA  VAIKLG  GAY++T  
Sbjct: 181 ITEINRLAALAHWVLPGLSEGRLLTGFEDPADIAAFYLDQGAEAVAIKLGPHGAYYRTHL 240

Query: 241 SEGFLEGCRVDRVVDTVGAGDGFAVGVISGILDGLSYKDAVQRGNAIGALQVQAPGDMDG 300
            +GF+ G  V  VVDTVGAGDGFAVG+IS +L+  S+ DAV+R N IG+  VQ+ GDM+G
Sbjct: 241 DQGFVAGVPVQTVVDTVGAGDGFAVGMISALLENHSFADAVRRANWIGSRAVQSRGDMEG 300

Query: 301 LPTREKLASFLSA 313
           LPTR ++ S   A
Sbjct: 301 LPTRSEMVSEFEA 313


Lambda     K      H
   0.317    0.135    0.399 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 312
Number of extensions: 16
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 324
Length of database: 328
Length adjustment: 28
Effective length of query: 296
Effective length of database: 300
Effective search space:    88800
Effective search space used:    88800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory